Anti-bacterial agents are developed by identifying unique targets not present in mammalian cells and then identifying a drug to exploit that difference such that the bacterial cells are killed or neutralized while mammalian cells are left intact and unaffected. The goal of successful anti-bacterial drug therapy is to limit toxicity in the patient while maximizing the ability of the drug to invade the bacterial cells and neutralize those cells as selectively as possible. The major classes of anti-bacterial drugs available today target a variety of different cellular components and functions of bacteria such as the cell wall, protein synthesis, cell metabolism, DNA synthesis, and the bacterial cell membrane. Each of these target cellular components or functions is related in some way to the disease process of bacterial infections that involves first colonization of the bacteria, invasion of host cells, production of cellular toxins or inflammatory agents, and a host response to those toxins or agents.
A fundamental process of all living cells, including bacteria, is the secretion of proteins across membranes. The majority of proteins that are secreted are synthesized as a precursor with an N-terminal signal sequence (or leader peptide) of about 16-24 amino acids in length. This leader sequence serves to promote recognition of the protein by the secretory apparatus of the cell and facilitates movement across the membrane. The leader sequence is subsequently processed by a leader peptidase to remove the sequence and allow release of the mature or active protein. Recent research has indicated that in the case of bacteria, there are several systems for secreting proteins and some of these systems have unique leader peptidases associated with their cognate secreted proteins. One of these systems is known as the type 2 secretion system which promotes extracellular secretion of bacterial factors such as toxins and colonization pili that are the hallmarks of the mechanisms that promote virulence of pathogenic bacteria. Pili mediate the binding of bacteria to host tissues and most pili are composed of a major protein subunit that polymerizes to form a pilus.
The type 2 secretion systems of most bacteria involve a type 4 pilin for pilus formation and type 4 pilin-like proteins for secretion of toxins and other factors associated with bacterial virulence and destruction of host tissue and enhancement of bacterial growth in the host. Highly related type 4 pili serve as the major colonization factors for up to 50 different gram-negative bacterial species and type 4 pilin-like proteins have been found for a growing number of gram-positive bacteria as well. Type 4 pili are composed of a polymerized structure of type 4 pilin. The pilin is synthesized as a prepilin with a leader peptide that is very different from those of typical secreted proteins. A type 4 specific leader peptidase is required to process a type 4 prepilin leader sequence to allow secretion of the mature protein. Importantly, this secretion system including the type 4 leader peptidase itself is only found in bacteria and is not present in humans or other potential hosts of infection. Furthermore, it has been shown that mutating the type 4 prepilin peptidase (TFPP) renders the bacterium avirulent (March & Taylor (1998) Mol. Microbiol. 29:1481-1492).
The type 4 signal peptide is highly conserved across all type 4 prepilin or prepilin-like proteins and is composed of 6 to 25 highly charged amino acids at the N-terminus followed by approximately 20 predominately hydrophobic amino acids. Cleavage occurs between the two domains immediately C-terminal of an invariant glycine and before the new N-terminal amino acid that is usually a methionine or a phenylalanine. Unlike cleavage of standard signal peptide by signal peptidase I, wherein the cleavage occurs on the periplasmic side of the inner membrane, processing by a type 4 peptidase occurs on the cytoplasmic side of the inner membrane (Strom & Lory (1993) Ann. Rev. Microbiol. 47:565-596). Previous mutational analysis and protease inhibitor evidence from studies of pilD of Pseudomonas aeruginosa and protein alignment analysis of the type 4 peptidase family suggested two pairs of cysteines in cytoplasmic domain 1, the largest cytoplasmic domain, to be involved in the protease active site of the enzyme (Strom, et al. (1993) Proc. Natl. Acad. Sci. USA 90:2404-2408). These data resulted in the categorization of type 4 prepilin peptidase (TFPP) family as a type of cysteine protease (Strom, et al. (1994) Meth. Enzymol. 235:527-540).
Using mutant constructs of TcpJ, a type 4 prepilin peptidase of Vibrio cholerae, residues essential for cleavage activity of the bacterial protease TFPP were identified as two aspartic acid residues (LaPointe & Taylor (2000) J. Biol. Chem. 275:1502-10). Screening assays to identify agents targeting these residues have been suggested (U.S. Pat. No. 6,887,677).
Dequalinium is a quaternary ammonium cation commonly available as the dichloride salt. The bromide, iodide, acetate, and undecenoate salts are known as well. Dequalinium chloride is a topical bacteriostat of use in the treatment of mouth and vaginal infections.

Analogs of dequalinium have been described for use in inhibiting the growth of and metastasis cancer cells (U.S. Pat. No. 6,974,871 and U.S. Pat. No. 6,790,962).